amber-developers: energy conservation

From: Jun Wang <>
Date: Mon, 14 Jan 2008 18:03:05 -0800 (PST)

Hi, all,

recently I am checking energy conservation of the program sander and
pmemd. I use the topology and restart file in amber9/benchmark/jac. I
turned off the temperature and pressure coupling. Shake is also turned
off. But I found the total energy of the isolated system drops gradually.
Who can help me to explain why this happened?

the following is the input file I used:
   ntx=7, irest=1,
   ntc=1, ntf=1, tol=0.0000001,
   ntpr=1, ntwr=10000,
   dt=0.0005, vlimit=0.0,
   ntt=0, temp0=300.,

Jun Wang, Ph.D.
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
Phone: (949) 824-9562
Received on Wed Jan 16 2008 - 06:07:21 PST
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